Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes Aegypti

The incomplete genome annotation of non-model organisms hampers molecular and translational studies. The divergent nature of transposable elements (TEs) has also limited their study by high-throughput proteomics. Proteomics informed by transcriptomics (PIT) is suited to non-model organisms and TEs because peptides are identified using transcriptomic, not genomic, data. We used PIT in the mosquito Aedes aegypti, vector for the (re-)emerging dengue, chikungunya, yellow fever and Zika viruses. We identify hotspots of incomplete genome annotation, and find that poor sequence and assembly quality do not explain annotation gaps. We develop criteria for the characterisation of proteomically active TEs and demonstrate that protein expression does not correlate with a TE’s genomic abundance. Finally, we identify Phasi Charoen-like virus as an unrecognised contaminant of Aag2 (Ae. aegypti) cells. We therefore present the first proteomic characterisation of mobile genetic elements, and provide proof-of-principle that PIT can evaluate a genome’s annotation to guide annotation efforts.